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Protocols

BAMBE specifications

Information


Unique identifier OMICS_04243
Name BAMBE
Alternative name Bayesian Analysis in Molecular Biology and Evolution
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 2.03
Stability Beta
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline BAMBE Team
  • person_outline Bret Larget
  • person_outline Donald Simon

BAMBE citations

 (4)
library_books

Erythroderma and extensive poikiloderma – a rare initial presentation of dermatomyositis: a case report

2018
PMCID: 5866516
PMID: 29571300
DOI: 10.1186/s13256-018-1618-y

[…] ture. Marcus and Wooldridge reported the case of a 23-year-old woman with progressive erythema involving her entire body who later developed proximal muscle weakness, tenderness, and poikiloderma []. Bambe described a 10.5-year-old girl with muscle weakness, joint stiffness, Raynaud phenomenon, poikiloderma, and scleroderma-like skin []. After that several cases were reported of which the latest w […]

library_books

The Gap Procedure: for the identification of phylogenetic clusters in HIV 1 sequence data

2015
BMC Bioinformatics
PMCID: 4634160
PMID: 26538192
DOI: 10.1186/s12859-015-0791-x

[…] oadly speaking, phylogenetics is the study of evolutionary relationships among organisms or taxon []. There are a number of programs for inferring phylogenies including, but not limited to, PAUP* [], BAMBE [], BEAST [], PHYLIP [] RAxML [] and MrBayes []. These relationships can be represented using a phylogenetic tree wherein branch lengths commonly reflect the estimated number of nucleotide subst […]

library_books

Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

2008
Int J Plant Genomics
PMCID: 2375977
PMID: 18483574
DOI: 10.1155/2008/683509

[…] best-performing software in a maximum likelihood setting. In a Bayesian framework, the basic perturbation schemes were described early [] and recently updated []. Three popular programs are MrBayes, BAMBE [], and BEAST []. Among all these programs and approaches, PHYML, GARLI, and BEAST are probably among the most efficient programs in terms of computational speed, handling of large data sets and […]

call_split

Cloning and characterization of cDNAs encoding putative CTCFs in the mosquitoes, Aedes aegypti and Anopheles gambiae

2005
BMC Mol Biol
PMCID: 1174870
PMID: 15985163
DOI: 10.1186/1471-2199-6-16
call_split See protocol

[…] eighbor or Fitch (5000 trees), a consensus tree determined using Consense and the tree drawn using Drawgram. The MultAlin alignment was also submitted to Tree-Puzzle [] with 200,000 replicates and to BAMBE [] with 200,000 cycles and 20,000 burn-in. […]

Citations

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